Naruto: Master of the Legendary Pokemon
by MasterBrattan
Summary: A Naruto/Pokemon Xover of a different kind. What happens when the Legendary Pokemon get sealed inside Naruto as well as the Kyuubi.
1. The Sealing

**Naruto: Master of the Legendary Pokémon**

A/N: A Naruto/Pokémon Xover of a different kind. What would happen if all the legendaries get sealed along with the Kyuubi inside of Naruto. Btw, people, just bear with me. I'm very new to actually writing fan fiction, having spent most of my time reading. This is just an idea that popped into my head and may have or may have not been inspired by the other various Naruto/Pkmn crossovers out there. This will be a Mass Harem fic, involving all female legendaries (in human form of course). All of the legendaries, except Latios, will be female. (Mewtwo: WHAT!!!?!?). Rotom will be counted as a legendary. Naruto will get a few human girls, including Hinata, but not limited to her. I'll get opinions from you guys on whom else should be in the harem. I'd like for each Pokémon to have their own special weapon, to pass onto Naruto later, and would like some ideas. Groudon already has a warhammer.

Disclaimer: I do not own Pokémon or Naruto.

"Talking"

"**Kyuubi, Boss Summon, Arceus in Pokeform, Naruto in Kyuubi/Pokémon mode talking, jutsu, Pokemoves"**

'_Thinking_'

Mewtwo, Lugia talking

_Letters, messages_

_Place skips_

"_**Kyuubi/Arceus**_"_Mewtwo/Lugia_ "_others_" all talking to Naruto

Chapter 1: The Sealing

_In a far off dimension…_

"**All right, is everyone here?**" a tall, white, horse-like being asked.

There were a variety of "yes, Arceus."s from the various creatures gathered.

"**Very well**" Arceus said.

The leader and matriarch of the legendary Pokémon looked out over the others that were gathered. All 36 had arrived for their vacation. Everyone had brought their various items and weapons. Dialga, Palkia, and Giratina had their respective orbs, Arceus had all 16 of her plates, Rotom had various appliances, and everyone else had random type based tools.

"**Palkia, seal the items in your pocket dimension!**" Arceus commanded.

"Right away," a large pinkish dragon answered as she met the request.

Arceus opened up a dimensional hole as everyone got set for travel. The Pokémon all flew through the hole for worlds unknown, not knowing what they will find, or that they were heading for an adventure that they never expected.

_In a completely different dimension…_

"**ROOAAARRRRRR!!!!!**" bellowed a massive fox with nine lashing tails.

"We must hold off the beast until the Hokage arrives!" yelled a random ninja.

'_No duh' _thought another one.

Shinobi from Konoha, the Village Hidden in the Leaves, threw everything they could at rampaging demon. But it was to no avail, weapons could not penetrate the beast's hide, jutsus of every element didn't even phase the fox as it approached. Unknown to everyone, a hole opened up above the clearly one-sided battle. Several creatures flew out, shocked at what they saw.

What the hell is going on here?! yelled out a tall purple and lavender cat.

"**I don't know, Mewtwo, but one thing is clear. Stop that Ninetales!**" ordered Arceus.

The Pokémon launched their attack to help the ninja. A large white golem and a massive reptilian beast threw themselves forward first. The two, known as Regigigas and Groudon, were the heaviest and sought to do some serious damage by hitting first. A long green dragon, known as Rayquaza, wrapped around a tail. Not the best idea.

"AAAHHH!!!" she screamed as she got lashed about with the tail.

The others kept using their attacks at max power, but it was useless, the beast was too big, even for Arceus to do any good. Groudon's claws could barely make a scratch. All in all, the enraged fox didn't even sense the Pokémon in their attempts to fight him. Mew, a small pink cat, looked up from her attempt to chew on an ear, only to see…

"Is that a giant Politoed?" she asked, seriously confused. "Smoking a pipe?"

"Seems like it!" Latios, a blue dragon, answered while unleashing an Ice Beam.

There was a flash of light, and the Pokémon could feel the Kyuubi tense up beneath them. They all looked ahead to see what could bring such a reaction in something so large. Floating behind the 'Politoed', was a large demonic specter.

What the Hell? shouted out Lugia.

"**A very appropriate term to use" **Arceus responded, slightly shaken by the new player in the game.

"Friend of yours, Darkrai" asked Articuno with a small, frightened smirk.

"…" was the Dark-Type's response, or lack of.

The demonic specter reached out towards the fox, taking notice of the beings scattered over its back. The Legendary Pokémon tensed as the fox demon let out an anguished roar as its soul was torn from it. No sooner did they all breathe a sigh of relief that they noticed that they were sharing in the fox's fate. With no time to protest, everything went black, with no one even knowing of the creatures from another dimension.

End of Chapter One

A/N: sorry if the battle with the Kyuubi seems rushed, but I'm sure we've all read millions of times in all the other fics. Plus, writing is not my strong suit, so bear with me. Any flames will be blocked by Groudon and the Fire-Types. I also ask for help on the human forms for the Legendary Pokémon. Mewtwo's will look like Anabel, since they've got the same color scheme. Latias will look like Bianca, except for pink hair. Darkrai will, inevitably, look like Storm, with maybe a darker complexion. And the hairstyle will be like Shippuden's Ino. Kyuubi will still be male though.


	2. Six Years Later

**Naruto: Master of the Legendary Pokémon**

A/N: Hey everyone, thank you for your reviews. I'm glad this was well met, only surprised no one commented on Mewtwo's reaction to finding out he's going to be a female in this.

Darkca: Naruto will only have the whisker marks. As for the Pokémon abilities, only when he fully taps into their power.

Ace of hell: thank you

Dragon Man 180: Thanks for the Mew idea, and on the birds. Though for them, I'll just leave the wings on the back, with the ability to become cloaks. As for Hinata getting an Eevee, I thought I'd do the same with all the human girls in the harem, just not Eevee's. Each girl will get a Pokémon that suits them best. I was also thinking of adding an anthro female Eevee to the harem, maybe two, one shiny, one not. All Pokémon will be able to switch between evolved forms. I will also be adding evolved forms for Eevee for the types it has not been given yet, at least what I would give.

Edd1460: I'll do that. Btw, where in the manga will I find Renji, I've found him on Wikipedia, but have no idea how his sword works. I'm not a much of a Bleach fan, but may start looking into it.

adngo174: Darkrai will speak a lot more in this fic. Glad you liked that though.

twilight dragon god: The Pokémon are sealed into Naruto.

Disclaimer: I do not own Naruto or Pokémon.

Chapter 2: Six years Later

It has been six years to the day that a ferocious demon was defeated by the greatest Hokage Konoha has ever seen. It was a day for celebrating the victory over the Kyuubi no Kitsune, and a day for mourning the loss of the shinobi who lost their lives. But for one young boy, it was a day of torment and fear.

'_Why are they doing this? I didn't do anything to them!'_ the young boy cried to himself.

"Kill the demon!" "Make it pay for taking our beloved Yondaime!" were just a few of the angry shouts directed at the target of their anger. (A/N: Sheesh, these scenes are so overdone, but harder to write than it looks.)

Their target was the young boy, barely six years old. He ran through streets, trying to get away, but he still couldn't miss the glares and sneers given to him by the villagers. An Anbu shinobi wearing a dog mask looked up from his little orange book, he watched as the child ran by, followed by his pursuers. He then looked back down to resume his reading.

'_None of my concern, the little beast deserves it.' _He thought.

The boy ran into an alley way, hoping to lose the villagers, but came to a dead end. His right arm was hanging by his side, useless as the shoulder had been pierced with a kunai earlier. His face was caked with blood, the blood dripping from his head when he had been hit with a club. His spiky blond hair was soaked with the red liquid of life. His cheeks were covered in dirt and blood, obscuring three whisker marks on each side. His once-white shirt, now covered in grime from a lack of washing, was full of tears and nearly in shreds. His shorts were nearly two sizes to big on him, equally torn. He turned around to try and get out, only to find the six villagers and two shinobi who had been chasing him. He was trapped, he couldn't get away, he was too hurt to try and fight back.

"Why are you doing this to me?" he cried, tears in his crystal blue eyes, "I didn't do anything to you!"

"You know exactly what you did, filthy demon!" one of the villagers snarled at him.

"This is for everyone you killed. Time to finish what the Yondaime started!" yelled another.

The villagers started to close in on the child, who curled up into a ball and hoped the pain would end quickly.

_Within Naruto's mindscape_

"This is the tenth time this week they've tried killing him!" Darkrai yelled.

"What!? But it's only Monday!" a small being with lightning bolts for arms cried.

"It's not his fault all those people died! It's yours, you big meanie!" a small yellow fairy with a star shaped headed shouted in the direction of a large cage.

"**Grrrrrr!!**" came the reply.

"**Rotom, Jirachi, calm down! Fox, Shut up!**" Arceus commanded. "**I, for one, have had enough! I'm going out there to put an end to this now!**"

_Back in the real world_

The villagers were closing in on the boy, when what appeared to be white chakra started to pour forth from him. The boy passed out from the pain, becoming oblivious to what was happening. The villagers watched as the chakra formed into a large horse-like creature. It had a green face and red eyes, with what appeared to be a long bony crest on the back of its head. The villagers also noticed yellow appendages coming from its sides.

"**WHAT THE FUCK DO YOU PEOPLE THINK YOU'RE DOING TO THIS CHILD!?**" it screamed at them.

One stupid villager shouted back, "This is no child! It's a damn demon and it deserves to die!"

"If you're going to protect it, you'll die to!" yelled one of the shinobi. "**Katon:**** Gouryuuka no Jutsu**!"

He breathed out a giant stream of fire, it taking on the form of a dragon. Arceus merely cocked an eyebrow at the attack.

"**Hyper Voice.**" She said, taking a deep breath.

Suddenly the creature let out an enormous scream, snuffing out the fire dragon and knocking the boy's attackers out of the alley.

"What is the meaning of this!?" an old man shouted.

"**Ah, so the Third Hokage finally shows. These people, and I use the term loosely, have attacked this child, the one called Naruto.**"

"Who are you, and what are you doing here?" the Hokage asked.

"**Take us somewhere more private and we shall talk. While you're at it, call your shinobi council, leave the civilians alone for now.**" Arceus replied.

"ANBU, take these people to Ibiki. Let him remind them what happens to those that break the law. Someone get Naruto and get him to the hospital." The Hokage ordered.

"**Don't you touch him**!" Arceus hissed as an ANBU wearing a platypus mask reached for Naruto. "**I will get him myself**!"

Before anyone could say or do anything, Arceus started to glow. When the glow died down, there in place of the unfamiliar creature, stood a woman. Her long blond hair went down to her hips, her eyes seemed to glow red, and her skin seemed to have an ethereal glow to it. Her bust was a cup size bigger than that of Tsunade's, while her clothes seemed to be an exact match. Everyone was stunned by the beauty before them, even as she placed her hands over Naruto. Her hands took on a blue-green glow and within a couple of minutes, the glow died down and all damage to Naruto had been healed.

"Shall we go now, and have our talk with your council?" she asked.

"Of course, if you will follow me." The Hokage answered, shaking of his shock. '_and maybe I can find out why you're so protective of Naruto._'

As the Hokage lead the woman to the council meeting room in the Hokage tower, he could only wonder what the future held for Naruto, and Konoha.

End of Chapter 2

A/N: I hope you readers enjoyed this chapter, even if the action was a bit slow. If you want to picture Arceus's human form, picture Tsunade with longer hair, red eyes, and a slightly bigger bust. As for the shinobi council, I writing to where they see Naruto for who he is. Though Sarutobi's teammates and Danzo, I haven't decided. Tune in for the next chapter when Arceus confronts the council, introduces herself and the other legendaries, and speaks with Naruto when he wakes up (as well as some threatening of the Kyuubi).


	3. Of Meetings

**Naruto: Master of the Legendary Pokémon**

A/N: Once again, I thank everyone who has read and reviewed this story. Like all authors, I appreciate the positive feedback I have received.

Mabscottsville: personally, I think the jury's still out on Rotom's status as a Legendary. But it is being added as one in this because the ability to possess machines may come in useful later.

Ok, the human girls who are being added to the harem and their Pokémon partners are as follows.

Hinata – Eevee, Azuril

Hana – Snubull, Houndour

TenTen – Smeargle, Magnemite

Kin – Zubat, Nidoran (F)

Tayuya – Chatot, Nidoran (M)

Isaribi – Magikarp, Feebas

Sasame – Gible, Trapinch

FemHaku – Swinub, Snorunt

Yugito – Meowth, Skitty

If anyone has anymore or different ideas, let me know. Though the girls will have no more than two Pokémon partners.

Disclaimer: I do not own Naruto or Pokémon.

"Talking"

"**Kyuubi, Boss Summon, Arceus in Pokeform, Naruto in Kyuubi/Pokémon mode talking, jutsu, Pokemoves"**

'_Thinking_'

'Mewtwo, Lugia talking'

_Letters, messages_

_Place skips_

"_**Kyuubi/Arceus**_" '_Mewtwo/Lugia_' "_others_" all talking to Naruto

"_Naruto talking back"_

Chapter 3: Of Meetings

It was late when the shinobi council had finally gathered in the meeting chambers. All the clan heads were there; Hyuuga, Uchiha, Nara, Yamanaka, Akimichi, Inuzuka, Aburame, Haruno, and Higurashi. Danzo and the former teammates of the Sandaime Hokage were there as well.

"Hokage-sama, why are we all here?" yawned a bored looking Nara Shikaku.

The old man sighed, "Some of the villagers have just tried to kill Naruto again tonight."

The response was split into two sides; everyone except Danzo, Uchiha Fugaku, and the Hokage's two teammates, Homura and Koharu, were outraged. Everyone had yet to notice the strange guest who bore a striking resemblance to the Slug Sannin. Unfortunately, her presence was noticed by Danzo.

"Sarutobi, who is this woman here with you and why is she holding the demon brat?" he questioned, glaring at said woman and brat with his one good eye.

The room grew quiet as the heavy pressure of killing intent started up. The levels were like nothing any of the ninja present had ever felt before. Some of the older nin could nearly feel the pressure threatening to cause their hearts to burst.

"You will not call the child a demon in my presence again," the woman said, her voice dangerously low, "or I will insure that you will not live to regret it."

"Arceus-san, please calm down, this is why we called this meeting." Sarutobi pleaded, nearly passing out himself from the pressure generated.

"Fine." Was the curt reply as she released her KI.

"Very well, everyone, as I have just said, Naruto was nearly killed again. By the time the ANBU and I had gotten there, Arceus here had taken care of the guilty parties. She then managed to heal all of his injuries…" the Hokage started.

"If I may interrupt, I think I should just tell them the whole story." Arceus said.

The next few hours were filled with Arceus telling them about the Pokémon world, how she and the other legendaries took their vacation and wound up sealed inside Naruto. She told them of the attempts on his life, the beatings, being fed spoiled food. With a glare at Sarutobi she added how he had been kicked out of the orphanage at four years old.

"How could you not notice such a travesty?" she asked as she finished her tale.

The aged Hokage just put his head in his hands, feeling lower than ever that he had failed Naruto.

Sensing this, Arceus continued, "If you truly wish to make it up to him, begin his ninja training now. Since we are sealed inside of him, we will begin training him in his Pokémon powers. Now since I don't trust anyone too much, I request the kunoichi with the snake mask to …"

"Out of the question! That brat, being trained by the snake bitch! They will destroy the village together!" Fugaku snarled.

"From what I've seen, that may not be a bad thing." Arceus replied coolly. "One more thing, **Judgment!**"

Everyone froze as a light gray ball formed over her outstretched hand and was launched into the Uchiha's chest, knocking him to the floor.

"How dare you…" he started.

"Sit down now, Fugaku!" Sarutobi roared as he snapped out of his funk. "Arceus-san, that was uncalled for!" he continued as his temper started to cool off.

"What? That was at a low power setting, anything stronger would have knocked him through the wall." Arceus protested.

"Regardless, what was that attack anyways?" the old man asked as he sent an ANBU to retrieve Anko.

"That was my own special attack. Only I can use it, and 15 other Legendaries have an attack only they can use."

"I have a question Arceus-san. Why do you request Anko's help in training Naruto in your arts?" asked Hyuuga Hiashi.

"We do not need help in the Pokémon training," Arceus replied with a snicker. "Sorry, inside joke. We need help in the ninja arts, and my reasons should be obvious." She continued, her voice going flat.

"Fair enough, and now, I have a question." Inuzuka Tsume jumped in, trying to break the tension. "How is Naruto is asleep through all this?"

"Oh that! When I healed him, I used Hypnosis to keep him asleep so he could at least meet the others. I also felt…"

SLAM! "The sexy and single Mitarashi Anko reporting for duty, sir!" a loud and exuberant voice rang out as the door was kicked in.

"Loud, troublesome woman." (A/N: we all know who this is.)

_In Naruto's mindscape_

(A/N: ok, I have grown tired of Arceus talking to the council and have decided to jump to Naruto meeting the other Pokémon. The results of the first meeting will be revealed towards the end of the chapter.)

Drip, Drip, Drip. The sound of dripping water caused Naruto to wake up. The first thing he noticed was that he was standing in a sewer, ankle deep in water.

"I guess they finally decided to throw me away." The little boy sighed.

"Hee, hee hee!" came a very amused and cute-sounding giggle.

"Who's there?" Naruto cried out, starting to get frightened.

"Don't worry, Naruto-kun, I won't hurt you." A feminine voice purred in his ear.

Naruto jumped as he spun around, and promptly fell on his butt. What he saw was a small pink cat with blue eyes, eyes that sparkled with mischief. The strange thing that he noticed was that it was floating.

"What are you? Where are we?" Naruto asked.

"My name is Mew and I'm a Pokémon. As for where we are, I'll just have to introduce you to the others first. Now follow me!" she shouted as she settled into his arms.

"How am I going to follow you if I'm carrying you?"

"I'll just tell you where to go. Now, walk straight ahead. Turn left here, make another left, left again, and another left."

Naruto followed the directions Mew was giving him when he noticed something.

"Hey! We just went in one big circle!" Naruto pouted at being tricked.

"Sorry, couldn't resist. I promise I'll show you the way this time, on one condition." Mew apologized, floating out of his arms and turning to face him.

"What's that?" Naruto asked, fearing the condition.

"Tag! You're It!" Mew laughed as she flew off.

Naruto laughed too as he chased the small cat, never losing track of her. He kept chasing her until…

"Gotcha!" he shouted as he finally caught her.

His eyes widened as he took in the view before him. Mountains, lakes, fields, forests, all kinds of places were here in the sewers. But, in the back, there was a large cage. Naruto was so entranced by the sights that he never heard Mew sigh in contentment as she snuggled into his arms.

"Everyone, time to come out and see Naruto-kun!" she called out.

If Naruto had been amazed by the scenery, he was absolutely stunned by the multitude of creatures that came forth. There were all kinds of birds and dogs, even a few dragons. There were a few creatures that Naruto couldn't figure out, as they did not look like any animal he had ever seen.

"Hello there Naruto-kun, my name is Articuno." A large blue bird said. It had a long tail and a crest with three points on its head. There was also a bit of a chill coming from it.

'My name is – ' a large purple and lavender cat started as its words seemed to run throughout the entire area.

"What happened?" Naruto screamed as he started crushing Mew in his arms.

"Naruto-kun, choking, not breathing!" Mew wheezed out.

"Sorry, Mew-neechan. But what happened?"

"Mewtwo tried speaking to you by telepathy, which means to communicate through the mind. But it seems to have been a bad idea considering where we are." A tiny hedgehog with a flower on its back chirped up.

"Who are you? And what do you mean 'where we are' ?" Naruto asked.

At this, all the creatures tensed up, not knowing how to answer this.

"My name is Shaymin, and to answer your other question: What do you know of the Kyuubi?"

End Chapter Three

A/N: and I'm going to stop right there for now. This part is getting just a bit long for me right now, plus I don't know how to go about having the Pokémon tell him about the Kyuubi. Hopefully, the action will start to pick up soon. I do wish to know if there are any other girls out there that anyone wants added to the harem. If I add Sakura, she'll get an Oddish I'm not sure what else. If Ino is added, she'll get Budew and Abra(I won't be cruel enough to give her Spoink). I was thinking of giving Naruto an actual bloodline, but felt it would be overkill. I do, however, have an idea that I want to use later. He will be descended from the Kuchiyose clan; if you want to use this idea for a bloodline, let me know and I'll send you the details. Hope you enjoyed this chapter.


	4. Moving in with Anko

**Naruto: Master of the Legendary Pokémon**

A/N: Once again, I thank all those who have reviewed; it just shows what you think of my story.

Ok, I have the harem planned out, just written in a notebook somewhere for my benefit. You guys have to wait and see as the girls are added.

Disclaimer: If I owned Pokémon, Ash would be a better trainer. If I owned Naruto, Naruto would have actually been trained by Kakashi and ero-sennin. Sadly, I own neither one of them.

Chapter 4: Moving in with Anko and training begins

"My name is Shaymin, and to answer your other question: What do you know of the Kyuubi?"

Naruto looked confused. "The Forth Hokage killed it when it attacked six years ago, didn't he?"

The Pokémon all shared sad looks, knowing this was not the case.

"Naruto-kun, we have no doubt that the Yondaime was strong, but even he did not have the strength to kill such a creature." Articuno began.

"Does that mean it's still out there?! We have to tell someone!" Naruto started to panic.

"Naru-chan, calm down. It has been defeated, so there is no danger." Mewtwo continued.

"If it isn't dead, then what happened to it?"

"You see that cage back there?" Shaymin asked. Naruto nodded.

"We'll tell the truth when we reach it, we want to introduce you to everyone. Now, follow me!" Shaymin finished as she hopped onto Naruto's head.

"Um, you're not going to make me go in circles like Mew did, are you?"

Mew couldn't help but scratch the back of her head at the looks the other three gave her.

"Don't worry, I'll make sure you go the right way." Shaymin reassured the boy.

The group of five started walking across a field, Naruto carrying Mew and Shaymin, Mewtwo floating along, and Articuno hovering overhead. They had only made it a third of the way across when they met three large dogs. One was yellow with a purple cloud on its back, the second was brown with red marks on its face, and smoke coming out of its back. The third was blue, with a purple mane, a crystal coming from its head, and twin tails curling around to the front.

"Hello there, Naruto-kun, my name is Raikou." Said the yellow dog.

"I'm Suicune, and this is Entei." The blue dog spoke up.

"I can introduce myself, you know." Entei growled.

"Yeah, yeah. So, where are you guys going?"

"Nice to meet you." Naruto greeted with a small bow. "We're going to that cage back there where Shaymin's going to tell me about the Kyuubi. Want to come?"

"We'd love to. Safety in numbers after all." Raikou answered.

Everyone started off again, Naruto missing the shared look between the dogs. Along the way, he met Articuno's friends Zapdos, a yellow bird with spiky feathers, and Moltres, an orange bird who appeared to be on fire. They were following along with Articuno hovering above the group on the ground. They were walking past a forest when a small green fairy, and a strange bird flew out to meet them. The bird was blue and yellow with ring like wings and a moon shaped head.

"Hi, I'm Celebi" the green fairy said.

"My name is Cresselia. Pleased to meet you Naruto-kun." The bird said in a melodious voice.

"Hello, um, how does everyone know my name?" Naruto asked.

"We know a lot about you, and we'll tell you at the cage." Celebi answered.

The group was walking through a clearing next to a lake where they met the three sprites: Azelf, Mesprit, and Uxie. Each had two tails, but different heads. Azelf's was blue with a small point coming out of the back, while Mesprit's was pink with four ear-like appendages. Uxie had a yellow head that looked like a pumpkin (A/N: at least it does to me). She always kept her eyes closed lest the person she looks at loses their memory. They met up with Groudon and Heatran, both of whom emerged from a volcano. Groudon was bipedal, covered in spikes, and had a reptilian look to her. Heatran walked on all fours and looked turtle-like. Naruto wound up carrying Mew in his arms, Shaymin on his head, Uxie was clinging to his right arm and Mesprit to his left. Azelf just settled to hang on his back looking over his shoulder.

"Naruto-kun, are you ready to meet Darkrai?" Azelf said, pointing upwards.

Naruto looked up, and saw a terrifying sight, at least in his six-year old mind.

"A Ghost!" he screamed, running to hide behind Groudon's leg.

He had peeked around to find a strange scene; everyone was chuckling, the ghost was off in a corner with a blue cloud of depression over it (A/N: think Brock when Ivy's name was said), and Mew was turning blue. WHAT?

"Sorry, Mew nee-chan!" Naruto apologized as he let up on his grip on the blue-turning-pink cat.

"That's…alright,…Naruto-kun." Mew wheezed out.

"Naruto, that's no ghost. That's Darkrai, one of our friends." Shaymin said, shaking off her amusement.

Naruto walked up to the Pitch-Black Pokémon, and shifting Mew to one arm, put a hand on her shoulder. She looked up at him.

"I'm sorry, Darkrai. I didn't mean to scream like that"

"It's okay, Naruto-kun. I know I can look scary sometimes, sorry if I scared you"

"I'm not so scared anymore, when I get a better look, you look pretty cool."

The ever-growing group met up with Rotom in what appeared to be an abandoned building, while they found Jirachi in a valley with Stonehenge like structures. Rayquaza flew down from the top of a very tall tower, and Deoxys was located near a meteor crash site. Regirock, Regice, Registeel, and Regigigas were discovered near some ruins. Naruto was stunned when he met the four Regi, mostly Regigigas on account of how big she was. The group had been walking along the shore of an ocean when…SPA-LOOSH! A large blue whale with large fins breached from the water, carrying two small water fairies, and followed by a sea bird with hand like wings.

"Hello there, young Naruto. My name is Lugia" said the sea bird.

"I'm Kyogre." The whale said.

"I'm Phione, and this is Manaphy."

Phione had a small red gem on her chest, two blue spots above her eyes, a ball on her head, and one antenna attached to the ball. Manaphy had four yellow spots above her eyes, and two antennas.

"Pleased to meet all of you, now could someone tell me how there is an ocean here?" Naruto asked.

"All in good time. Uxie, Mesprit, Celebi, Jirachi; let's get Kyogre." Azelf said.

The five all flew around the beached whale, and using their psychic powers, lifted her up and started to carry her. Before long, they had reached the cage. Along the way, they had been joined by Ho-oh, Latios(the only male in the group), Latias(his twin sister), Dialaga, Palkia, and Giratina. The cage had a piece of paper on it with the kanji for 'seal'. However, before anyone could say anything…

"**So, my jailer finally comes to visit me. Any last words before I rip you to shreds!**"

Not waiting for those last words, a huge claw shot out of the cage, heading for Naruto. The young blond had lost all control of his legs, unable to run or get out of the way. He had shut his eyes, waiting for it all to end.

"**Release me this instant!**" the voice raged.

Naruto looked up to see what had happened. The claw had not finished its decent because Groudon and Regigigas had rushed to intercept it, each grabbing a toe/finger.

"**Crush Grip**"

"Metal Claw"

The two attacks caused the beast to pull back his injured digits, roaring out in pain and frustration. All the Pokémon decided to get out of range, in case he tried to attack again.

Letting go of Mew, Naruto looked around at the gathered Pokémon. He had to know now.

"Why is the Kyuubi here? Where is here?" the young boy asked, tears of frustration welling up in his eyes.

"**Naruto-kun, the Kyuubi couldn't be killed. The only way to stop it seems to have been to seal it away. The fox, and all of us, are sealed away inside of you.**" Giratina said, remorse in her voice.

Naruto's eyes widened in shock, it suddenly all made sense. The harsh words, the hate-filled glares, the abuse, everything.

"Am I really a demon then? Did I really kill all those people?"

"**Of course not, dear child. You are merely the prison.**" A new voice said, one that radiated ultimate power. "**You are nothing more than a good little boy, who has been treated wrongly for something he had nothing to do with.**"

Naruto had turned around to see the new speaker, and saw a large white horse like creature.

"Who are you?" he asked in complete awe.

"**My name is Arceus, the very first Pokémon. While I'm at it, I do not believe the fox was fully in control that night.**"

"WHAT!!!" was the major response.

Instead of answering any questions, Arceus turned towards the cage.

"**Double Team**." She said.

Instantly, there were 17 Arceus's, each one had taken on a different color, one for each Pokémon type.

"**Judgment.**" 17 orbs shot out at the fox, hitting him right in the face.

"**GRAAAAAHHHH!!!!**" he yelled, before falling over.

Slowly, the fox started to stir. When he had opened his eyes, all the anger and malice was gone, only to be replaced by gratitude and remorse.

"**Thank you, for releasing that man's control over me. And Naruto, I deeply apologize for everything that had happened to you because of me.**"

"I forgive you, I guess, you seem different now than what people say, but I don't know what's going on."

"**We will tell you later, Naruto-kun. But now, it's time to wake up and talk to the Hokage.**" Arceus interrupted, sending Naruto back into consciousness.

_Tower in Forest of Death, back in real world_

Anko and Sarutobi watched as Naruto sat up in the bed, rubbing his eyes and yawning at the same time. Anko could hardly keep from squealing at the cute sight.

"Naruto, how are you feeling?" the Hokage asked.

"I'm fine, jiji, I just want to know why you didn't tell me about the fox, and the Pokémon."

"Naruto, I wanted to, but I wanted to protect you. As for the Pokémon, I didn't know about them myself until recently. I must ask you now, what do you plan to do now that you know about the fox?"

"I'm going to become the best ninja in the village and show everyone that I'm not a monster!" Naruto shouted with the utmost confidence. "And then I'll become the greatest Hokage ever!"

"Well said, gaki." Anko said.

"Now Naruto, I want you to get a good night's sleep. Tomorrow, we will be getting you ready for the Academy next week, when you will begin your ninja training."

"Alright, jiji."

"Don't worry kid, I'll be here tonight in case you need something." Anko informed the blond jinchurikki.

"Who are you?" Naruto asked.

"My name is Mitarashi Anko, and you'll be staying here with me while you're in the Academy. And until you can get your own place after you begin your career as a shinobi."

"Okay, Anko-neechan. Good Night!"

_The next morning_

"Wake up, Gaki!"

Naruto woke up with a start as he felt someone jump on the bed he was in. He noticed it was Anko, wearing her trenchcoat from yesterday, as well as black pants and a red shirt.

"Alright kid, we're going to go meet up with the Hokage so we can get you ready for the Academy. So start getting ready."

The area around Naruto's stomach started to glow and when it died down, a woman was standing there. She had long blond hair with streaks of green, and red eyes. She wore a green shirt that barely contained her G-cup sized breasts. She wore blue pants over equally shapely hips.

"I'll join you two." Arceus said.

"Do you really think that is necessary?" Anko asked.

"Anko, the fools who can't see past the Kyuubi are the same fools who can't see past your former sensei. How do you think they will act seeing you and Naruto together?"

"The Hokage will be there –"

"Yes, and given his record with Naruto, I have little faith in him. Anko, I will not tolerate the way they treat Naruto, nor will I tolerate the way they treat you. Now let's go!" Arceus had finished the talk while holding Anko's chin in her hand.

_The Hokage tower_

It was still fairly early in the morning when the Hokage and a young boy of around 11 were waiting for our trio. The boy had jet black hair and dark eyes, with some lines near them. Before too much longer, Anko, Arceus, and Naruto showed up.

"Good day, Anko-san, Naruto-kun, Arceus-san. I'm glad you could show up. I want - "

"Sama." Arceus interrupted.

"Excuse me."

"Sarutobi, you are to refer to me as –Sama. For three reasons: one; I have lived for more than an eternity, making me older than you. Two; I am a goddess, out ranking your title as Hokage. Three; considering what Naruto has gone through in his life, especially the _last two years, _you have not earned enough of my respect."

"As you wish, Arceus-sama. Now, I want to introduce you to Uchiha Itachi. He will be joining us in our errands today to get Naruto prepared for the Academy."

Arceus took a good look at Itachi, her eyes glowing slightly. A few seconds later, they stopped.

"Well, I see we'll get along better than your father. Your soul has less of a taint to it."

"He did forbid me to come on this trip. But I am a shinobi of the village and my orders come from the Hokage. Plus I wish to see Naruto get ready, as my little brother is already set for the Academy."

With that little exchange, the group of five set out. Their first stop was a clothing store for civilians, since Naruto wasn't a shinobi yet. Of course, as Naruto walked in…

"Get out of here demon! I already told you that I won't serve the likes of you!" the shop keeper shouted, before noticing the village leader behind the boy.

"If you will not serve Naruto-kun here, then you will not receive patronage from me. Nor will anyone else shop here if I can help it."

The group left the shop, ignoring the pleas of the shopowner. When they were outside, Itachi proposed an idea to the Hokage.

"Hokage-sama, if I may, I wish to put a genjutsu on this shop in order to deter business here."

"Make it so, Itachi-kun."

The Uchiha prodigy went through same handsigns and slammed his hand against the top of the doorframe.

"So, Itachi, just what will this jutsu do?" Anko asked.

"It will make the clothes inside the store appear to be unbareable and very unpleasant for purchase."

"Like what, patched and torn, and moth-eaten." Arceus asked.

"Worst. They will be nothing but green spandex and orange leg warmers. There will be a standee of Maito Gai, complete in Good Guy pose © with the ping in his teeth. The worst part will be no matter where you are in the store, it will appear to be facing you. Playing over the loudspeaker will be that song he sang at the karaoke bar."

"That is just plain evil. I like it!" Anko, clearly enjoying the idea, cackled.

"What song is this?" Sarutobi asked.

Anko pulled out a tape recorder and pushed the Play button.

_I'm not wearing underwear today!_

_No I'm not wearing underwear today!_

_Not that you probably care_

_Much about my underwear._

_Still nonetheless I gotta saaaaaay!_

_That. I'm. Not. Wear. Ing. Un. Der. Wear. Tooo. Daaaaaaaaaaaay!_

(A/N: if you want to hear this, go to YouTube and plug in 'Real Ninjas' into the search engine. I do not own this song, btw.)

"That has got to be one of the scariest things I have ever heard, and I'm older than time itself." Arceus said.

Finally understanding what was going on, seeing as how that song scared him, gave his opinion on the matter. Ah, the innocence of a six-year-old.

"Wait, does this mean that man is going to go out of business? I don't want him to get in trouble because of me. Please take off that gen-thingy." Naruto started begging, throwing out the one jutsu all children know, the Puppy Dog Eye no Jutsu.

Even the iron will of Itachi could not hold up to that look. With a glance at Sarutobi, who nodded his consent, Itachi removed the illusionary technique.

"Sometimes I think you are too nice for your own good, kid." Anko said, shaking her head.

_Elsewhere in the village, sometime later_

The group soon found their way towards another store where they hoped they would have better luck, or else Arceus would have something to say. Of course, they were going to find out how powerful she could be.

"You little demon! You will pay for what you did to my family!" some random nin charged at Naruto with a kunai, oblivious to those around him.

He threw the kunai, only for Arceus to knock it aside with her hand. She charged at the man, grabbing him by the neck and lifting him into the air.

"Who do you think you are? Attacking a child with your village leader right here?" she demanded him.

"Shut up bitch! You have no idea what that monster did! He killed my family, and now he's controlling the Hokage!"

Arceus's eyes were glowing the whole time. She then made her opinion known.

"The only monster here I see, is you. I have looked into your soul, and I must say, what I have seen is truly disturbing. I see you have killed, and not in defense of your village. You have killed people who were no threat to you, people who live in Fire country. Children, civilians, women, and people who could not defend themselves. Also, you have raped many women and children, both male and female. You have done this in other villages, sometimes disguised as a shinobi from another village. You have stolen, pillaged, and raided homes. For crimes such as these, **I sentence you to Hell!**"

People started to scream as the ground opened up, fire shooting out and the howling of demons could be heard. Some tried to climb out, only to slink back in when given a hard look from Arceus. The man screamed when she dropped him into the pit, the demons tearing at him. The screams faded as the ground closed back up. Arceus turned back to the group.

"Alright, let's get back to what we were doing."

The group found a different clothing store, hoping for his sake, that he would be more hospitable. When they walked in, the store owner looked up and smiled, not even batting an eye when he saw Naruto.

"Hokage-sama!" he greeted, "I'm glad you're here!"

The man then went into how the civilian council was forcing the few shop owners who liked Naruto to refuse him service, though they still tried to help him. Even if it was by putting edible food near their trash for him.

"So, what can I do for you?" he asked at the end of his tale.

"We need to pick up some clothes for Naru-chan here," Arceus said, breaking her glare from Hiruzen, "preferably non-shinobi for now. We can wait until he becomes a ninja to get that kind of gear. Now as for what we need, I say three weeks worth of clothes. We need shirts, shorts, pants, socks, boxers, maybe jackets and coats, and maybe a week's worth of shoes."

"Very good, Arceus-sama, do you have any colors in mind?" the storeowner asked.

"Black and red would work well." Itachi said in his monotone voice.

"I think green, brown, and orange looks good." Anko added.

"Perhaps blue, yellow, and white." The Hokage said.

"All good colors for shirts, but at least blue and black for the shorts and pants," The man said, feeling that many colors would not go well. "as for socks, white would be best."

"Does all that sound good to you, Naruto?" Arceus asked the young blond, who could only nod, just a little overwhelmed at all the clothes he was going to get.

"Can I pick out my shoes myself, and my boxers?" he asked.

"Of course you can. We can't not let you have a say in what you're going to wear." Sarutobi said.

"Um, what are boxers anyways?" the chibi blonde asked.

No one could keep a straight face at the innocent question as They all burst out laughing.

"Boxers are underwear, Naruto-kun" Itachi said, trying to hide his own amusement.

Naruto had gotten to choose 14 pairs of boxers: some were plain colors, such as red, blue, or black. Some had different designs on them; shuriken, foxes, clouds, even bowls of ramen. His shoes were all plain themselves, mostly blue or black. Everyone felt they had gotten enough clothes when they all had their arms full with bags, though Arceus had Naruto in one of hers.

"If you ever need anything else, don't be afraid to come on by." The shop owner called out as they left.

"Don't worry, we will!" Arceus called back.

"Bye-Bye!" Naruto waved.

The group had been wandering for a while when they heard a loud rumbling. Everyone turned to look at Arceus, who was looking at Naruto with wide eyes.

"Heh, Heh, Heh." He chuckled sheepishly, scratching the back of his head. "I guess I'm getting a little hungry."

"I suppose it is getting close to lunch." Sarutobi said, smiling at Naruto. "Does anyone have any suggestions?"

"Somewhere with dango!"

"I know a place that serves an excellent shark-fin soup."

Naruto started to look down, having never been in any of the stores or restaurants. Arceus, on the other hand, never needed to eat before in her life.

"Anywhere you choose will be fine, as long as they let Naru-chan in, or else." She said with finality.

The group eventually settled on a barbeque restaurant run by the Akamichi clan.

A/N: I wish to thank all of those who have waited patiently for this update, and for those who didn't, I thank for giving me that much needed nudge when I got lazy. I apologize if this chapter was a little slow at first, but I felt the need to get this stuff through.

The pairings include: Naruto x Hinata x Ino x Sakura x Tenten x Yakumo x Hana x Anko x Kurenai x Hanabi x Moegi x FemHaku x Kin x Tayuya x Karin x Isaribi x Sasame x Temari x Hokuto x Fuu x Yugito x Karui x Samui x Shion x Toki x Haruna x Koyuki x Articuno x Zapdos x Moltres x Mewtwo x Mew x Raikou x Entei x Suicune x Ho-oh x Lugia x Celebi x Regirock x Regice x Registeel x Groudon x Kyogre x Rayquaza x Latias x Deoxys x Jirachi x Rotom x Uxie x Mesprit x Azelf x Dialga x Palkia x Heatran x Regigigas x Giratina x Cresselia x Phione x Manaphy x Darkrai x Shaymin x Arceus x Haruka (anthro Eevee) x Kasumi (shiny anthro Eevee). (Thank kami for Kage Bunshin. This is in no particular order.) I do have plans for Neji, Chouji, Kiba, and Lee, but they will have to wait. Getting a girl will be too troublesome for Shikamaru, and as for Sasuke, I'll just leave the whole Orochimaru thing to your imaginations, cause I will not write such a thing. The only yaoi I can handle is Leon/D from Petshop of Horrors. (It just fits.) Btw, who came up with Itachi's obsession with pocky, and Sasuke's with tomatoes.


	5. AN: Really Sorry

**Naruto: Master of the Legendary Pokémon**

Attention all my readers; first of all, I would like to thank everyone for sticking with this and continuously putting me under their favorites. I would also like to apologize for not updating this fic for nearly two years, school (which I've graduated from ITT), work, and getting caught up in reading. I also feel that I may have bitten off more than I can chew with the story line. So I will try to rewrite this, but make a few changes.

I will involve the Unova legendaries as well.

No Pokémon in harem, just human girls.

No special weapons from the Pokémon, mostly a shape-shifting Mew.

Though they will arrange for several swords from other dimensions.

No good Kyuubi.

Naruto will end up with three Pokémon; Eevee, Vulpix, and Zorua.

Each girl will wind up with more than three Pokémon.

Only Pokémon to have human forms will be Arceus (his right as the Pokémon god), and Mew (being a shape-shifter).


End file.
